American biologist James A. Shapiro in his book Evolution: A View from the 21st Century (2011) has written that evolutionary mechanisms such as horizontal gene transfer, symbiogenesis, whole genome doubling and natural genetic engineering are all non-Darwinian and can not be fitted into the modern evolutionary synthesis as the modern synthesis is still working in a Darwinian framework. Shapiro believes many of these mechanisms fit better with a saltationist school rather than Darwin's strict advocacy of gradualism via "numerous, successive, slight variations".

Eugene Koonin has said that the neo-Darwinian synthesis is wrong.

See his papers Eugene Koonin, The Origin at 150: Is a new evolutionary synthesis in sight?" Trends in Genetics, 25(11), November 2009, pp. 473-475 and Eugene Koonin, Darwinian evolution in the light of genomics, Nucleic Acids Research, 37(4), 2009, pp. 1011-1034

He says in these papers:

See his papers Eugene Koonin, The Origin at 150: Is a new evolutionary synthesis in sight?" Trends in Genetics, 25(11), November 2009, pp. 473-475 and Eugene Koonin, Darwinian evolution in the light of genomics, Nucleic Acids Research, 37(4), 2009, pp. 1011-1034

He says in these papers:

In the post-genomic era, all the major tenets of the modern synthesis have been, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution.

The discovery of pervasive HGT and the overall dynamics of the genetic universe destroys not only the tree of life as we knew it but also another central tenet of the modern synthesis inherited from Darwin, namely gradualism. In a world dominated by HGT, gene duplication, gene loss and such momentous events as endosymbiosis, the idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable.

Equally outdated is the (neo-) Darwinian notion of theadaptive nature of evolution; clearly, genomes show very little if any signs of optimal design, and random drift constrained by purifying in all likelihood contributes (much) more to genome evolution than Darwinian selection.

Forests wrote:American biologist James A. Shapiro in his book Evolution: A View from the 21st Century (2011) has written that evolutionary mechanisms such as horizontal gene transfer, symbiogenesis, whole genome doubling and natural genetic engineering are all non-Darwinian and can not be fitted into the modern evolutionary synthesis as the modern synthesis is still working in a Darwinian framework. Shapiro believes many of these mechanisms fit better with a saltationist school rather than Darwin's strict advocacy of gradualism via "numerous, successive, slight variations".

Anyone who thinks that life on Earth is the product of a single mechanism is a fool. Few evolutionary biologists do. It's the relative contributions of the different mechanisms that's important. No one has yet demonstrated that Darwinian natural selection has been a minor mechanism. Mechanisms such as HGT complicate our attempts at phylogenetic reconstruction. They don't refute them. I also doubt that many evolutionary biologists think that all evolutionary change occurs at a single, constant rate. As far as Koonin goes, opinions are not evidence.

HGT does not fit well into the neo-Darwinian synthesis. Most scientists who have written on HGT are now calling for an extended synthesis or new totally new synthesis.

I also doubt that many evolutionary biologists think that all evolutionary change occurs at a single, constant rate

That is pretty much what the neo-Darwinists such as yourself believe, you claim evolution can only occur by gradualism and you deny saltationism or larger jumps.

As far as Koonin goes, opinions are not evidence.

wbla3335 funny as you offer yourself nothing but an opinion. Your opinions are not worth anything, considering you don't even back any of your claims up with any kind of evidence. Are you a scientist? What peer reviews do you have out? Koonin has many out.

Here is another scientific paper:

The new biology: beyond the Modern Synthesis

Michael R Rose1* and Todd H Oakley2

Abstract: The last third of the 20th Century featured an accumulation of research findings that severely challenged the assumptions of the "Modern Synthesis" which provided the foundations for most biological research during that century. The foundations of that "Modernist" biology had thus largely crumbled by the start of the 21st Century. This in turn raises the question of foundations for biology in the 21st Century.

Anyone who thinks that life on Earth is the product of a single mechanism is a fool. Few evolutionary biologists do.

Well that is pretty close to what the neo-Darwinian synthesis advocates, according to those narrow minded scientists evolution is driven by less than 5 mechanisms!

That sounds like an opinion.

Forests wrote:

It's the relative contributions of the different mechanisms that's important.

Of course it is, but the neo-Darwinists deny most mechanisms.

That sounds like an opinion.

Forests wrote:

No one has yet demonstrated that Darwinian natural selection has been a minor mechanism.

There are many scientific papers out there showing natural selection is not a major mechanism.

If there were many scientific papers out there "showing" natural selection is not a major mechanism, more people would be of your view. If you ever become a scientist, you will need to be more careful how you say things.

HGT does not fit well into the neo-Darwinian synthesis. Most scientists who have written on HGT are now calling for an extended synthesis or new totally new synthesis.

To extrapolate what happens in the prokaryotic world to all of life is not a wise thing to do.

Forests wrote:

I also doubt that many evolutionary biologists think that all evolutionary change occurs at a single, constant rate

That is pretty much what the neo-Darwinists such as yourself believe, you claim evolution can only occur by gradualism and you deny saltationism or larger jumps.

How on Earth do you get that from what I said?

Forests wrote:

As far as Koonin goes, opinions are not evidence.

wbla3335 funny as you offer yourself nothing but an opinion. Your opinions are not worth anything, considering you don't even back any of your claims up with any kind of evidence. Are you a scientist? What peer reviews do you have out? Koonin has many out.

I'm a retired scientist (evolutionary biologist) and educator. I don't have as many publications as Koonin, but quantity of publications is not always a good measure of contribution. This is not to say that Koonin is a bad scientist. On the contrary. He has done a lot of good work, but the more I learn of his more recent publications, the more I get the impression that he sees his views more as a vehicle to wider recognition that to truth. That's just my opinion.

You are still at an early point in what hopefully will be a lifetime of learning. Don't rush to judgment. Too many minds slam shut when that happens. But my opinions are not worth anything.

No wbla3335 it is not just my personal opinion, it is an opinion backed up with scientific evidence via scientific papers (papers which you have ignored).

Eugene Koonin, in his research paper, titled "Darwinian evolution in the light of genomics", published 12 Feb 2009, says:

"Now, 50 years after the consolidation of the Modern Synthesis, evolutionary biology undoubtedly faces a new major challenge and, at the same time, the prospect of a new conceptual breakthrough"....."By contrast, the insistence on adaptation being the primary mode of evolution that is apparent in the Origin, but especially in the Modern Synthesis, became deeply suspicious if not outright obsolete, making room for a new worldview that gives much more prominence to non-adaptive processes"......"Collectively, the developments in evolutionary genomics and systems biology outlined here seem to suggest that, although at present only isolated elements of a new, 'postmodern' synthesis of evolutionary biology are starting to be formulated, such a synthesis is indeed feasible. Moreover, it is likely to assume definitive shape long before Darwin's 250th anniversary"

Michael R Rose and Todd H Oakley, in their research paper, titled "The new biology: beyond the Modern Synthesis" published on 24 November 2007

wrote that The last third of the 20th Century featured an accumulation of research findings that severely challenged the assumptions of the "Modern Synthesis" which provided the foundations for most biological research during that century. The foundations of that "Modernist" biology had thus largely crumbled by the start of the 21st Century. This in turn raises the question of foundations for biology in the 21st Century".

This paper presents some of the recent challenges to theModern Synthesis of evolutionary theory, which has dominatedevolutionary thinking for the last sixty years. The focus ofthe paper is the challenge of soft inheritance - the idea that variations that arise during development can beinherited. There is ample evidence showing that phenotypic variations that are independent of variations in DNAsequence, and targeted DNA changes that are guided by epigenetic control systems, are important sources ofhereditary variation, and hence can contribute to evolutionary changes. Furthermore, under certain conditions, themechanisms underlying epigenetic inheritance can also lead to saltational changes that reorganize the epigenome. These discoveriesare clearly incompatible with the tenets of the Modern Synthesis, which denied any significant role forLamarckian and saltational processes. In view of the data that support soft inheritance, as well as other challengesto the Modern Synthesis, it is concluded that that synthesis no longer offers a satisfactory theoretical framework forevolutionary biology.

There is also a more in depth debate about on all this on another forum: